Hello,
I have a bunch of RNA-Seq files (single-end runs) to be aligned to a reference genome. I plan to do that by Bowtie2. However, I see that there are 3 different assembly files - softmasked.fa, hardmasked.fa and the .fa file with no description. I wonder if someone could tell me which one to go for?
And whether if there will be differences in the final differential expression analysis based on the choice of assembly files.
Appreciate your help and time.
-Alan
I have a bunch of RNA-Seq files (single-end runs) to be aligned to a reference genome. I plan to do that by Bowtie2. However, I see that there are 3 different assembly files - softmasked.fa, hardmasked.fa and the .fa file with no description. I wonder if someone could tell me which one to go for?
And whether if there will be differences in the final differential expression analysis based on the choice of assembly files.
Appreciate your help and time.
-Alan